Making Commandargs Comma Delimited or Parsing Spaces

Write access to commandArgs?

How about simply overwriting it with your own definition, e.g.

commandArgs <- function(trailingOnly=FALSE) { 
    args<- c("/foo/bar", "baz") 
    # copied from base:::commandArgs
    if (trailingOnly) {
        m <- match("--args", args, 0L)
        if (m) 
            args[-seq_len(m)]
        else character()
    }
    else args
} 

How do I parse command line arguments in Bash?

Bash Space-Separated (e.g., --option argument)

cat >/tmp/demo-space-separated.sh <<'EOF'
#!/bin/bash

POSITIONAL_ARGS=()

while [[ $# -gt 0 ]]; do
  case $1 in
    -e|--extension)
      EXTENSION="$2"
      shift # past argument
      shift # past value
      ;;
    -s|--searchpath)
      SEARCHPATH="$2"
      shift # past argument
      shift # past value
      ;;
    --default)
      DEFAULT=YES
      shift # past argument
      ;;
    -*|--*)
      echo "Unknown option $1"
      exit 1
      ;;
    *)
      POSITIONAL_ARGS+=("$1") # save positional arg
      shift # past argument
      ;;
  esac
done

set -- "${POSITIONAL_ARGS[@]}" # restore positional parameters

echo "FILE EXTENSION  = ${EXTENSION}"
echo "SEARCH PATH     = ${SEARCHPATH}"
echo "DEFAULT         = ${DEFAULT}"
echo "Number files in SEARCH PATH with EXTENSION:" $(ls -1 "${SEARCHPATH}"/*."${EXTENSION}" | wc -l)

if [[ -n $1 ]]; then
    echo "Last line of file specified as non-opt/last argument:"
    tail -1 "$1"
fi
EOF

chmod +x /tmp/demo-space-separated.sh

/tmp/demo-space-separated.sh -e conf -s /etc /etc/hosts

Output from copy-pasting the block above

FILE EXTENSION  = conf
SEARCH PATH     = /etc
DEFAULT         =
Number files in SEARCH PATH with EXTENSION: 14
Last line of file specified as non-opt/last argument:
#93.184.216.34    example.com

Usage

demo-space-separated.sh -e conf -s /etc /etc/hosts

---

Bash Equals-Separated (e.g., --option=argument)

cat >/tmp/demo-equals-separated.sh <<'EOF'
#!/bin/bash

for i in "$@"; do
  case $i in
    -e=*|--extension=*)
      EXTENSION="${i#*=}"
      shift # past argument=value
      ;;
    -s=*|--searchpath=*)
      SEARCHPATH="${i#*=}"
      shift # past argument=value
      ;;
    --default)
      DEFAULT=YES
      shift # past argument with no value
      ;;
    -*|--*)
      echo "Unknown option $i"
      exit 1
      ;;
    *)
      ;;
  esac
done

echo "FILE EXTENSION  = ${EXTENSION}"
echo "SEARCH PATH     = ${SEARCHPATH}"
echo "DEFAULT         = ${DEFAULT}"
echo "Number files in SEARCH PATH with EXTENSION:" $(ls -1 "${SEARCHPATH}"/*."${EXTENSION}" | wc -l)

if [[ -n $1 ]]; then
    echo "Last line of file specified as non-opt/last argument:"
    tail -1 $1
fi
EOF

chmod +x /tmp/demo-equals-separated.sh

/tmp/demo-equals-separated.sh -e=conf -s=/etc /etc/hosts

Output from copy-pasting the block above

FILE EXTENSION  = conf
SEARCH PATH     = /etc
DEFAULT         =
Number files in SEARCH PATH with EXTENSION: 14
Last line of file specified as non-opt/last argument:
#93.184.216.34    example.com

Usage

demo-equals-separated.sh -e=conf -s=/etc /etc/hosts

---

To better understand ${i#*=} search for "Substring Removal" in this guide. It is functionally equivalent to `sed 's/[^=]*=//' <<< "$i"` which calls a needless subprocess or `echo "$i" | sed 's/[^=]*=//'` which calls two needless subprocesses.

---

Using bash with getopt[s]

getopt(1) limitations (older, relatively-recent getopt versions):

• can't handle arguments that are empty strings
• can't handle arguments with embedded whitespace

More recent getopt versions don't have these limitations. For more information, see these docs.

---

POSIX getopts

Additionally, the POSIX shell and others offer getopts which doen't have these limitations. I've included a simplistic getopts example.

cat >/tmp/demo-getopts.sh <<'EOF'
#!/bin/sh

# A POSIX variable
OPTIND=1         # Reset in case getopts has been used previously in the shell.

# Initialize our own variables:
output_file=""
verbose=0

while getopts "h?vf:" opt; do
  case "$opt" in
    h|\?)
      show_help
      exit 0
      ;;
    v)  verbose=1
      ;;
    f)  output_file=$OPTARG
      ;;
  esac
done

shift $((OPTIND-1))

[ "${1:-}" = "--" ] && shift

echo "verbose=$verbose, output_file='$output_file', Leftovers: $@"
EOF

chmod +x /tmp/demo-getopts.sh

/tmp/demo-getopts.sh -vf /etc/hosts foo bar

Output from copy-pasting the block above

verbose=1, output_file='/etc/hosts', Leftovers: foo bar

Usage

demo-getopts.sh -vf /etc/hosts foo bar

The advantages of getopts are:

1. It's more portable, and will work in other shells like dash.
2. It can handle multiple single options like -vf filename in the typical Unix way, automatically.

The disadvantage of getopts is that it can only handle short options (-h, not --help) without additional code.

There is a getopts tutorial which explains what all of the syntax and variables mean. In bash, there is also help getopts, which might be informative.

R command line passing a filename to script in arguments (Windows)

As I said in my comment, I would use Rscript instead of R CMD BATCH:

Rscript myscript.R batch.csv

where myscript.R contains:

args <- commandArgs(TRUE)
batch_args <- read.table(args[1], sep=",")
# loop over multiple runs

Passing multiple arguments via command line in R

After searching around, and avoiding to write a new package from the bottom up, I figured the best way to input multiple arguments using the package optparse is to separate input files by a character which is most likely illegal to be included in a file name (for example, a colon)

Rscript test.R --inputfiles fileA.txt:fileB.txt:fileC.txt etc...

File names can also have spaces in them as long as the spaces are escaped (optparse will take care of this)

Rscript test.R --inputfiles file\ A.txt:file\ B.txt:fileC.txt etc...

Ultimatley, it would be nice to have a package (possibly a modified version of optparse) that would support multiple arguments like mentioned in the question and below

Rscript test.R --inputfiles fileA.txt fileB.txt fileC.txt

One would think such trivial features would be implemented into a widely used package such as optparse

Cheers

batch mode quoted parameters parsing

Yeah, R CMD BATCH acts a little weird.

Try this instead:

R --slave --vanilla --file=test-parameters.R --args foo=2 bar=3 "s=string with spaces" > output

The --slave and --vanilla options might be replaced with more suitable options as needed.

Best way to parse command line arguments in C#?

I would strongly suggest using NDesk.Options (Documentation) and/or Mono.Options (same API, different namespace). An example from the documentation:

bool show_help = false;
List<string> names = new List<string> ();
int repeat = 1;

var p = new OptionSet () {
    { "n|name=", "the {NAME} of someone to greet.",
       v => names.Add (v) },
    { "r|repeat=", 
       "the number of {TIMES} to repeat the greeting.\n" + 
          "this must be an integer.",
        (int v) => repeat = v },
    { "v", "increase debug message verbosity",
       v => { if (v != null) ++verbosity; } },
    { "h|help",  "show this message and exit", 
       v => show_help = v != null },
};

List<string> extra;
try {
    extra = p.Parse (args);
}
catch (OptionException e) {
    Console.Write ("greet: ");
    Console.WriteLine (e.Message);
    Console.WriteLine ("Try `greet --help' for more information.");
    return;
}

Specifying arguments with spaces for running a python script

where "argument 1" is a single argument.

You've basically answered your own question there, "argument 1" is indeed a single argument.

In other words, you need to quote it, something like one of:

python testProgram.py "argument 1" 'argument 2'

This isn't actually a Python issue however, it depends on the shell that you're using to run the Python script.

For example, with bash, there are differences between the single and double quotes, the most important of which is probably the various expansions like $HOME - the single quoted variant does not do those expansions.

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